Heatmap
Volcano Plot of Significant Genes
Volcano Plot of All Expressed Genes
Enrichments with EnrichR
Upregulated in Mutant
## Uploading data to Enrichr... Done.
## Querying GO_Biological_Process_2018... Done.
## Querying KEGG_2019... Done.
## Parsing results... Done.
Downregulated in Mutant
## Uploading data to Enrichr... Done.
## Querying GO_Biological_Process_2018... Done.
## Querying KEGG_2019... Done.
## Parsing results... Done.
Pathway Visualisation
Toll Signalling Pathway
MAPK Signalling Pathway
Dorsal Target Genes
Dorsal Targets in the Mesoderm
Hypergeometric Test
q = nrow(zscores_meso)
m = nrow(zscores_meso)
n = nrow(counts(dds)) - nrow(zscores_meso)
k = nrow(ue)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0
Dorsal Targets in the Neuroectoderm
Hypergeometric Test
q = nrow(zscores_neuroecto)
m = nrow(zscores_neuroecto)
n = nrow(counts(dds)) - nrow(ue)
k = nrow(ue)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0
Dorsal Targets in the Ectoderm
Hypergeometric Test
q = nrow(zscores_ecto) - 1
m = nrow(zscores_ecto)
n = nrow(counts(dds)) - nrow(oe)
k = nrow(oe)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 4.851825e-05
Combined Heatmap
Session Info
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] png_0.1-7 VennDiagram_1.6.20
## [3] futile.logger_1.4.3 enrichR_3.0
## [5] fgsea_1.16.0 reactome.db_1.74.0
## [7] pathview_1.30.1 org.Dm.eg.db_3.12.0
## [9] msigdbr_7.2.1 ggrepel_0.9.1
## [11] cowplot_1.1.1 ggpubr_0.4.0
## [13] data.table_1.14.0 DT_0.17
## [15] forcats_0.5.1 dplyr_1.0.5
## [17] purrr_0.3.4 readr_1.4.0
## [19] tidyr_1.1.3 tibble_3.1.0
## [21] ggplot2_3.3.3 tidyverse_1.3.0
## [23] stringr_1.4.0 enrichplot_1.13.0
## [25] ReactomePA_1.34.0 clusterProfiler_3.18.1
## [27] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.58.0
## [29] rtracklayer_1.50.0 Biostrings_2.58.0
## [31] XVector_0.30.0 pheatmap_1.0.12
## [33] geneplotter_1.68.0 annotate_1.68.0
## [35] XML_3.99-0.6 reshape_0.8.8
## [37] lattice_0.20-41 gridExtra_2.3
## [39] RColorBrewer_1.1-2 GenomicFeatures_1.42.3
## [41] AnnotationDbi_1.52.0 knitr_1.31
## [43] DESeq2_1.30.1 SummarizedExperiment_1.20.0
## [45] Biobase_2.50.0 MatrixGenerics_1.2.1
## [47] matrixStats_0.58.0 GenomicRanges_1.42.0
## [49] GenomeInfoDb_1.26.7 IRanges_2.24.1
## [51] S4Vectors_0.28.1 BiocGenerics_0.36.0
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.1 tidyselect_1.1.0 RSQLite_2.2.6
## [4] htmlwidgets_1.5.3 BiocParallel_1.24.1 scatterpie_0.1.5
## [7] munsell_0.5.0 withr_2.4.1 colorspace_2.0-0
## [10] GOSemSim_2.16.1 highr_0.8 rstudioapi_0.13
## [13] ggsignif_0.6.1 DOSE_3.16.0 labeling_0.4.2
## [16] KEGGgraph_1.50.0 GenomeInfoDbData_1.2.4 polyclip_1.10-0
## [19] bit64_4.0.5 farver_2.1.0 rprojroot_2.0.2
## [22] downloader_0.4 vctrs_0.3.7 treeio_1.14.4
## [25] generics_0.1.0 lambda.r_1.2.4 xfun_0.22
## [28] BiocFileCache_1.14.0 R6_2.5.0 graphlayouts_0.7.1
## [31] locfit_1.5-9.4 bitops_1.0-6 cachem_1.0.4
## [34] DelayedArray_0.16.3 assertthat_0.2.1 scales_1.1.1
## [37] ggraph_2.0.5 gtable_0.3.0 tidygraph_1.2.0
## [40] rlang_0.4.10 genefilter_1.72.1 splines_4.0.5
## [43] rstatix_0.7.0 lazyeval_0.2.2 broom_0.7.6
## [46] checkmate_2.0.0 abind_1.4-5 BiocManager_1.30.12
## [49] yaml_2.2.1 reshape2_1.4.4 modelr_0.1.8
## [52] crosstalk_1.1.1 backports_1.2.1 qvalue_2.22.0
## [55] tools_4.0.5 ellipsis_0.3.1 jquerylib_0.1.3
## [58] Rcpp_1.0.6 plyr_1.8.6 progress_1.2.2
## [61] zlibbioc_1.36.0 RCurl_1.98-1.3 prettyunits_1.1.1
## [64] openssl_1.4.3 viridis_0.5.1 haven_2.3.1
## [67] fs_1.5.0 magrittr_2.0.1 futile.options_1.0.1
## [70] openxlsx_4.2.3 DO.db_2.9 reprex_2.0.0
## [73] hms_1.0.0 patchwork_1.1.1 evaluate_0.14
## [76] xtable_1.8-4 rio_0.5.26 readxl_1.3.1
## [79] compiler_4.0.5 biomaRt_2.46.3 crayon_1.4.1
## [82] shadowtext_0.0.7 htmltools_0.5.1.1 aplot_0.0.6
## [85] lubridate_1.7.10 DBI_1.1.1 formatR_1.8
## [88] tweenr_1.0.2 dbplyr_2.1.1 MASS_7.3-53.1
## [91] rappdirs_0.3.3 Matrix_1.3-2 car_3.0-10
## [94] cli_2.4.0 igraph_1.2.6 pkgconfig_2.0.3
## [97] rvcheck_0.1.8 GenomicAlignments_1.26.0 foreign_0.8-81
## [100] xml2_1.3.2 ggtree_2.4.2 bslib_0.2.4
## [103] rvest_1.0.0 digest_0.6.27 graph_1.68.0
## [106] rmarkdown_2.7 cellranger_1.1.0 fastmatch_1.1-0
## [109] tidytree_0.3.4 curl_4.3 Rsamtools_2.6.0
## [112] graphite_1.36.0 rjson_0.2.20 lifecycle_1.0.0
## [115] nlme_3.1-152 jsonlite_1.7.2 carData_3.0-4
## [118] viridisLite_0.4.0 askpass_1.1 fansi_0.4.2
## [121] pillar_1.6.0 KEGGREST_1.30.1 fastmap_1.1.0
## [124] httr_1.4.2 survival_3.2-10 GO.db_3.12.1
## [127] glue_1.4.2 zip_2.1.1 Rgraphviz_2.34.0
## [130] bit_4.0.4 ggforce_0.3.3 stringi_1.5.3
## [133] sass_0.3.1 blob_1.2.1 org.Hs.eg.db_3.12.0
## [136] memoise_2.0.0 ape_5.5